X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details PEG 550 MME, sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.98 α = 90
b = 156.26 β = 90
c = 271.2 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-02-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.3 39.12 99.7 0.081 -- -- 4.5 37932 37818 -999.0 -3.7 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.3 3.5 99.2 0.433 -- 2.3 4.5 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.3 40.0 -- -- 37932 35817 1882 99.77 -- 0.23302 0.23005 0.28943 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.3 3.385 -- 131 2589 0.274 0.35 -- 98.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 94.4
Anisotropic B[1][1] 2.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.06
r_scbond_it 0.578
r_mcangle_it 0.561
r_mcbond_it 0.305
r_nbd_refined 0.215
r_gen_planes_refined 0.003
r_chiral_restr 0.035
r_dihedral_angle_4_deg 16.127
r_dihedral_angle_3_deg 20.345
r_dihedral_angle_2_deg 38.93
r_dihedral_angle_1_deg 6.596
r_angle_refined_deg 0.528
r_bond_refined_d 0.002
r_nbtor_refined 0.316
r_xyhbond_nbd_refined 0.151
r_symmetry_vdw_refined 0.131
r_symmetry_hbond_refined 0.126
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12771
Nucleic Acid Atoms 0
Heterogen Atoms 89
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.700 data extraction
REFMAC5 version: 5.2.0003 refinement